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Low pH (5.5) nitrite-bound MSOX movie series dataset 3 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [1.83 MGy] - nitrite/NO intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 293 0.1 M Tris pH 7.3, 1.8 M Ammonium Sulphate
Crystal Properties Matthews coefficient Solvent content 2.72 54.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.21 α = 90 b = 104.21 β = 90 c = 64.37 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2022-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.855 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.23 45.12 99.1 0.031 0.999 10.7 5.1 114182 13.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.23 1.25 98.4 0.84 0.333 0.9 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.23 30 108320 5838 99.08 0.11549 0.11431 0.1146 0.13767 0.1378 RANDOM 17.696
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.22 -0.11 -0.22 0.7
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.575 r_dihedral_angle_3_deg 12.724 r_long_range_B_other 11.979 r_dihedral_angle_2_deg 11.333 r_scangle_other 9.101 r_dihedral_angle_1_deg 7.815 r_scbond_it 6.797 r_mcangle_other 6.476 r_mcangle_it 6.472 r_scbond_other 6.422
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.575 r_dihedral_angle_3_deg 12.724 r_long_range_B_other 11.979 r_dihedral_angle_2_deg 11.333 r_scangle_other 9.101 r_dihedral_angle_1_deg 7.815 r_scbond_it 6.797 r_mcangle_other 6.476 r_mcangle_it 6.472 r_scbond_other 6.422 r_mcbond_it 4.705 r_mcbond_other 4.665 r_rigid_bond_restr 3.842 r_angle_refined_deg 1.862 r_angle_other_deg 0.665 r_chiral_restr 0.1 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2562 Nucleic Acid Atoms Solvent Atoms 397 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling